<html><body><div style="color:#000; background-color:#fff; font-family:verdana, helvetica, sans-serif;font-size:12pt"><div>Dear Prof.</div><div><br></div><div>I have several questions about trjconv, please help me.</div><div><br></div><div>In my simulation is created 2 micelles.</div><div>1- When I do 3 steps of micelle clustering as follows:</div><div><br></div><div> a- <code>trjconv <span style="background-color: rgb(255, 255, 0);">-f md.xtc</span> -o a_cluster.gro<span style="background-color: rgb(255, 255, 0);"> -e 600000 </span>-pbc
cluster</code></div><div><code> b- </code><code>grompp <span style="background-color: rgb(255, 255, 0);">-f md.mdp</span> -c a_cluster.gro -o a_cluster.tpr</code></div><div><code> c- </code><code>trjconv <span style="background-color: rgb(255, 255, 0);">-f </span><span style="background-color: rgb(255, 255, 0);">md.xtc</span> -o a_cluster.xtc -s a_cluster.tpr
-pbc nojump</code></div><div><br><code></code></div><div>I view 2 micelles according to result of my simulation in VMD but in ngmx isn't view 2 micelles but just is view 1 micelle and reminder of monomers are collected in several groups in different places.</div><div>Is it right if my criterion be view in VMD and is my micelle clustering correct?<br><code></code></div><div><br></div><div>2- If I select surfactants for clustering group and system for output group in step (a) and I select system for output group in step (c), command g_clustsize doesn't work correct, consequently, I did under step and made a .xtc file only for surfactants: <br></div><div> <br></div><div> i- <span class="tab">trjconv -f md.trr -o md-surfactant.xtc -n index.ndx<br></span></div><div> <br></div><div>Then I did steps a, b and c for md-surfactant.xtc and in all of steps I selected surfactants for clustering and output
group. Next, I did g_clustsize and it answered me correct. <br></div><div>May I know that my way is correct, please?<br></div><div><br></div><div>3- By upper way I have 2 micelles that I got index.ndx file for cluster with maximum size by g_clustsize (maxcluster.ndx).</div><div>May I know how can I use from this for next calculation if I want consider only maximum cluster with all of system (water and ion) in calculations (for example rdf, gyration and etc)?<br></div><div><br></div><div>Please help me<br></div><div>Best Regards <br></div><div>Sara<br></div><div><br></div><div><br></div><div><br></div><div><br></div><div><br></div><div><br></div><div><br></div><div><br></div><div></div></div></body></html>